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Book ; Online: HUMAN SARS CoV-2 SPIKE PROTEIN MUTATIONS

Lalitha Guruprasad

2020

Abstract: The human SARS-CoV-2 spike protein sequences from Asia, Africa, Europe, North America, South America and Oceania were analyzed by comparing with the reference SARS-CoV-2 protein sequence from Wuhan-Hu-1, China. Out of 10,333 spike protein sequences ... ...

Abstract	The human SARS-CoV-2 spike protein sequences from Asia, Africa, Europe, North America, South America and Oceania were analyzed by comparing with the reference SARS-CoV-2 protein sequence from Wuhan-Hu-1, China. Out of 10,333 spike protein sequences analyzed, 8,155 proteins comprised one or more mutations. A total of 9,654 mutations were observed that correspond to 400 distinct mutation sites. The receptor binding domain (RBD) which is involved in the interactions with human ACE-2 receptor and causes infection leading to the COVID-19 disease comprised 44 mutations that included residues within 3.2 Å interacting distance from the ACE-2 receptor. The mutations observed in the spike proteins are discussed in the context of their distribution according to the geographical locations, mutation sites, mutation types, distribution of the number of mutations at the mutation sites and mutations at the glycosylation sites. The density of mutations in different regions of the spike protein sequence and location of the mutations in protein three-dimensional structure corresponding to the RBD are discussed. The mutations identified in the present work are important considerations for antibody, vaccine and drug development.
Keywords	Bioinformatics and Computational Biology ; SARS-CoV-2 ; Spike proteins ; receptor binding domain (RBD) ; mutations ; sequence and structural mapping ; covid19
Subject code	612
Publishing date	2020-08-20T11:17:57Z
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Evolutionary Relationships and Sequence-Structure Determinants in Human SARS Coronavirus-2 Spike Proteins for Host Receptor Recognition

Lalitha Guruprasad

2020

Abstract: Coronavirus disease 2019 (COVID-19) is a pandemic infectious disease caused by novel Severe Acute Respiratory Syndrome coronavirus-2 (SARS CoV-2). The SARS CoV-2 is transmitted more rapidly and readily than SARS CoV. Both, SARS CoV and SARS CoV-2 via ... ...

Abstract	Coronavirus disease 2019 (COVID-19) is a pandemic infectious disease caused by novel Severe Acute Respiratory Syndrome coronavirus-2 (SARS CoV-2). The SARS CoV-2 is transmitted more rapidly and readily than SARS CoV. Both, SARS CoV and SARS CoV-2 via their glycosylated spike proteins recognize the human angiotensin converting enzyme-2 (ACE-2) receptor. We generated multiple sequence alignments and phylogenetic trees for representative spike proteins of CoV and CoV-2 from various host sources in order to analyze the specificity in SARS CoV-2 spike proteins required for causing infection in humans. Our results show that two sequence motifs in the N-terminal domain; "MESEFR" and "SYLTPG" are specific to human SARS CoV-2 and pangolin SARS CoV. In the receptor binding domain (RBD), three sequence loops; VGGNY (loop 1), YQAGSTPC (loop 2), EGFNCY (loop 3) and a tethered disulfide bridge Cys480-Cys488 connecting loops 2 and 3 are structural determinants for the recognition of human ACE-2 receptor. The complete genome analysis of representative SARS CoVs from bat, civet, pangolin, human host sources and human SARS CoV-2 identified the bat genome (GenBank code: MN996532.1) and the pangolin SARS CoV genomes as closest to the recent novel human SARS CoV-2 genomes. The bat CoV genomes (GenBank codes: MG772933 and MG772934) are evolutionary intermediates in the mutagenesis progression towards becoming human SARS CoV-2.
Keywords	Bioinformatics and Computational Biology ; Severe acute respiratory syndrome coronavirus-2 ; complete genomes ; spike proteins ; multiple sequence alignment ; phylogenetic tree ; receptor binding domain ; covid19
Subject code	572
Publishing date	2020-04-27T07:23:30Z
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Taking stock of the mutations in human SARS-CoV-2 spike proteins

Lalitha Guruprasad / Gatta KRS. Naresh / Ganesh Boggarapu

Current Research in Structural Biology, Vol 6, Iss , Pp 100107- (2023)

From early days to nearly the end of COVID-19 pandemic

2023

Abstract: The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), causative agent of the coronavirus disease-2019 (COVID-19) has resulted in several deaths and severe economic losses throughout the world. The spike protein in the virus binds to the human ...

Abstract	The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), causative agent of the coronavirus disease-2019 (COVID-19) has resulted in several deaths and severe economic losses throughout the world. The spike protein in the virus binds to the human ACE-2 receptor in order to mediate virus-host interactions required for the viral transmission. Since first report of the SARS-CoV-2 sequence during December 2019 from patient infected with the virus in Wuhan, China, the virus has undergone rapid changes leading to mutations comprising substitutions, deletions and insertions in the sequence resulting in several variants of the virus that were more virulent and transmissible or less virulent but highly transmissible. The timely intervention with COVID-19 vaccines proved to be effective in controlling the number of infections. However, rapid mutations in the virus led to the lowering of vaccine efficacies being administered to people. In May 2023, the World Health Organization declared COVID-19 was not a public health emergency of international concern anymore. In order to take stock of mutations in the virus from early days to nearly end of COVID-19 pandemic, sequence analyses of the SARS-CoV-2 spike proteins available in the NCBI Virus database was carried out. The mutations and invariant residues in the SARS-CoV-2 spike protein sequences relative to the reference sequence were analysed. The location of the invariant residues and residues at interface of the protein chains in the spike protein trimer complex structure were examined. A total of 111,298 non-redundant SARS-CoV-2 spike protein sequences representing 2,345,585 spike proteins in the NCBI Virus database showed mutations at 1252 of the 1273 positions in the amino acid sequence. The mutations represented 6129 different mutation types in the sequences analysed. Besides, some sequences also contained insertion mutations. The SARS-CoV-2 spike protein sequences represented 1435 lineages. In addition, several spike protein sequences with mutations whose ...
Keywords	Human SARS-CoV-2 ; Spike protein ; Invariant residues ; Mutations ; Sequence analyses ; Three-dimensional structure analyses ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Ponatinib is a pan-BCR-ABL kinase inhibitor

Karunakar Tanneeru / Lalitha Guruprasad

PLoS ONE, Vol 8, Iss 11, p e

MD simulations and SIE study.

2013 Volume 78556

Abstract: BCR-ABL kinase domain inhibition can be used to treat chronic myeloid leukemia. The inhibitors such as imatinib, dasatinib and nilotinib are effective drugs but are resistant to some BCR-ABL mutations. The pan-BCR-ABL kinase inhibitor ponatinib exhibits ... ...

Abstract	BCR-ABL kinase domain inhibition can be used to treat chronic myeloid leukemia. The inhibitors such as imatinib, dasatinib and nilotinib are effective drugs but are resistant to some BCR-ABL mutations. The pan-BCR-ABL kinase inhibitor ponatinib exhibits potent activity against native, T315I, and all other clinically relevant mutants, and showed better inhibition than the previously known inhibitors. We have studied the molecular dynamics simulations and calculated solvated interaction energies of native and fourteen mutant BCR-ABL kinases (M244V, G250E, Q252H, Y253F, Y253H, E255K, E255V, T315A, T315I, F317L, F317V, M351T, F359V and H396P) complexed with ponatinib. These studies revealed that the interactions between ponatinib and individual residues in BCR-ABL kinase are also affected due to the remote residue mutations. We report that some residues, Met244, Lys245, Gln252, Gly254, Leu370 and Leu298 do not undergo any conformational changes, while the fluctuations in residues from P-loop, β3-, β5- strands and αC- helix are mainly responsible for ponatinib binding to native and all mutant BCR-ABL kinases. Our work provides the molecular mechanisms of native and mutant BCR-ABL kinases inhibition by ponatinib at atomic level that has not been studied before.
Keywords	Medicine ; R ; Science ; Q
Subject code	612
Language	English
Publishing date	2013-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Prediction of Certain Well-Characterized Domains of Known Functions within the PE and PPE Proteins of Mycobacteria.

Rafiya Sultana / Karunakar Tanneeru / Ashwin B R Kumar / Lalitha Guruprasad

PLoS ONE, Vol 11, Iss 2, p e

2016 Volume 0146786

Abstract: The PE and PPE protein family are unique to mycobacteria. Though the complete genome sequences for over 500 M. tuberculosis strains and mycobacterial species are available, few PE and PPE proteins have been structurally and functionally characterized. We ...

Abstract	The PE and PPE protein family are unique to mycobacteria. Though the complete genome sequences for over 500 M. tuberculosis strains and mycobacterial species are available, few PE and PPE proteins have been structurally and functionally characterized. We have therefore used bioinformatics tools to characterize the structure and function of these proteins. We selected representative members of the PE and PPE protein family by phylogeny analysis and using structure-based sequence annotation identified ten well-characterized protein domains of known function. Some of these domains were observed to be common to all mycobacterial species and some were species specific.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2016-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Structure based annotation of Helicobacter pylori strain 26695 proteome.

Swati Singh / Praveen Kumar Guttula / Lalitha Guruprasad

PLoS ONE, Vol 9, Iss 12, p e

2014 Volume 115020

Abstract: The availability of complete genome sequences of H. pylori 26695 has provided a wealth of information enabling us to carry out in silico studies to identify new molecular targets for pharmaceutical treatment. In order to construe the structural and ... ...

Abstract	The availability of complete genome sequences of H. pylori 26695 has provided a wealth of information enabling us to carry out in silico studies to identify new molecular targets for pharmaceutical treatment. In order to construe the structural and functional information of complete proteome, use of computational methods are more relevant since these methods are reliable and provide a solution to the time consuming and expensive experimental methods. Out of 1590 predicted protein coding genes in H. pylori, experimentally determined structures are available for only 145 proteins in the PDB. In the absence of experimental structures, computational studies on the three dimensional (3D) structural organization would help in deciphering the protein fold, structure and active site. Functional annotation of each protein was carried out based on structural fold and binding site based ligand association. Most of these proteins are uncharacterized in this proteome and through our annotation pipeline we were able to annotate most of them. We could assign structural folds to 464 uncharacterized proteins from an initial list of 557 sequences. Of the 1195 known structural folds present in the SCOP database, 411 (34% of all known folds) are observed in the whole H. pylori 26695 proteome, with greater inclination for domains belonging to α/β class (36.63%). Top folds include P-loop containing nucleoside triphosphate hydrolases (22.6%), TIM barrel (16.7%), transmembrane helix hairpin (16.05%), alpha-alpha superhelix (11.1%) and S-adenosyl-L-methionine-dependent methyltransferases (10.7%).
Keywords	Medicine ; R ; Science ; Q
Subject code	540
Language	English
Publishing date	2014-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Insights into the carbonic anhydrases and autotrophic carbon dioxide fixation pathways of high CO2 tolerant Rhodovulum viride JA756

Khandavalli, Lakshmi Venkata Naga Satya / Lalitha Guruprasad / Maaged Abdullah / Sasikala Chintalapati / Tushar Lodha / Venkata Ramana Chintalapati

Microbiological research. 2018 Oct., v. 215

2018

Abstract: Biofixation of CO2 is being extensively investigated to solve the global warming problem. Purple non-sulfur bacteria are fast growers that consume CO2 and produce beneficial biomass. Better the growth at higher CO2 levels, more efficient are the strains ... ...

Abstract	Biofixation of CO2 is being extensively investigated to solve the global warming problem. Purple non-sulfur bacteria are fast growers that consume CO2 and produce beneficial biomass. Better the growth at higher CO2 levels, more efficient are the strains for biofixation. Nine among fifty strains that were analyzed at elevated CO2 levels responded with better growth. Considering its enhanced growth at high CO2 and metabolic versatility, Rhodovulum viride strain JA756 was chosen to make further studies. Strain JA756 tolerates up to 50% (v/v) CO2 with its optimum between 20–40% (v/v), yielding a biomass of 3.4 g. L−1. The pattern of specific enzyme activity of carbonic anhydrase corresponded well with that of its growth. To gain insights into the genomic composition and genes related to carbonic anhydrases and CO2 fixation, draft genome sequencing of JA756 was carried out which revealed the presence of two non-homologous genes encoding for β and γ carbonic anhydrases, both of which are assumed to be implicated in maintaining intracellular inorganic carbon concentration at equilibrium. Most of the genes involved in the Calvin pathway, reductive tricarboxylic acid pathway, 3-hydroxypropionate bicycle and C4 pathways were found in the draft genome. While the experimental determinations of active roles of two of these pathways are still underway, the expression of key genes of Calvin and C4 pathway suggest their functional role in the organism. Owing to its metabolic versatility, JA756 can be advantageous for biological CO2 assimilation facilities located by the coastline, inland and also at wide ranges of CO2 concentrations.
Keywords	biomass ; C4 photosynthesis ; carbon ; carbon dioxide ; carbon dioxide enrichment ; carbon dioxide fixation ; carbonate dehydratase ; carboxylic acids ; genes ; genomics ; global warming ; Rhodospirillaceae ; Rhodovulum ; sequence analysis
Language	English
Dates of publication	2018-10
Size	p. 130-140.
Publishing place	Elsevier GmbH
Document type	Article
ZDB-ID	1189614-0
ISSN	1618-0623 ; 0944-5013
ISSN (online)	1618-0623
ISSN	0944-5013
DOI	10.1016/j.micres.2018.07.006
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The PE-PPE domain in mycobacterium reveals a serine α/β hydrolase fold and function

Rafiya Sultana / Karunakar Tanneeru / Lalitha Guruprasad

PLoS ONE, Vol 6, Iss 2, p e

an in-silico analysis.

2011 Volume 16745

Abstract: The PE and PPE proteins first reported in the genome sequence of Mycobacterium tuberculosis strain H37Rv are now identified in all mycobacterial species. The PE-PPE domain (Pfam ID: PF08237) is a 225 amino acid residue conserved region located towards ... ...

Abstract	The PE and PPE proteins first reported in the genome sequence of Mycobacterium tuberculosis strain H37Rv are now identified in all mycobacterial species. The PE-PPE domain (Pfam ID: PF08237) is a 225 amino acid residue conserved region located towards the C-terminus of some PE and PPE proteins and hypothetical proteins. Our in-silico sequence analysis revealed that this domain is present in all Mycobacteria, some Rhodococcus and Nocardia farcinica genomes. This domain comprises a pentapeptide sequence motif GxSxG/S at the N-terminus and conserved amino acid residues Ser, Asp and His that constitute a catalytic triad characteristic of lipase, esterase and cutinase activity. The fold prediction and comparative modeling of the 3-D structure of the PE-PPE domain revealed a "serine α/β hydrolase" structure with a central β-sheet flanked by α-helices on either side. The structure comprises a lid insertion with a closed structure conformation and has a solvent inaccessible active site. The oxyanion hole that stabilizes the negative charge on the tetrahedral intermediate has been identified. Our findings add to the growing list of serine hydrolases in mycobacterium, which are essential for the maintenance of their impermeable cell wall and virulence. These results provide the directions for the design of experiments to establish the function of PE and PPE proteins.
Keywords	Medicine ; R ; Science ; Q
Subject code	572
Language	English
Publishing date	2011-02-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Purification and characterization of a stable Kunitz trypsin inhibitor from Trigonella foenum-graecum (fenugreek) seeds

Oddepally, Rajender / Gopi Sriram / Lalitha Guruprasad

Phytochemistry. 2013 Dec., v. 96

2013

Abstract: Kunitz trypsin inhibitor was purified from the seeds of Trigonella foenum-graecum (TfgKTI) belonging to fabaceae family by ammonium sulphate precipitation, cation exchange, gel filtration and hydrophobic chromatography. Purity of the protein was analyzed ...

Abstract	Kunitz trypsin inhibitor was purified from the seeds of Trigonella foenum-graecum (TfgKTI) belonging to fabaceae family by ammonium sulphate precipitation, cation exchange, gel filtration and hydrophobic chromatography. Purity of the protein was analyzed by RP-HPLC and native-PAGE. SDS–PAGE analysis under reducing and non-reducing conditions showed that protein consists of a single polypeptide chain with molecular mass of approximately 20kDa. Mass spectroscopy analysis revealed that the intact mass of purified inhibitor is 19,842.154Da. One dimensional SDS gel was tryptically digested, resulting peptides were subjected to MALDI-TOF-MS analysis, and peptide mass fingerprinting (PMF) analysis of TfgKTI shows sequence similarity with Kunitz trypsin inhibitor in database search. Two dimensional electrophoresis identified presence of four isoinhibitors (pI values of 5.1, 5.4, 5.7 and 6.1). Kinetic studies showed that the protein is a competitive inhibitor and has high binding affinity with trypsin (Ki 3.01×10−9M) and chymotrypsin (Ki 0.52×10−9M). The TfgKTI retained the inhibitory activity over a broad range of pH (pH 3–10), temperature (37–100°C) and salt concentration (up to 3.5%). Far-UV circular dichroism measurements revealed that TfgKTI is predominantly composed of β-sheets (39%) and unordered structures (48%) with slight helical content (13%). TfgKTI retained over 90% trypsin inhibition upon storage at 4°C for over a period of six months.
MeSH term(s)	Aprotinin/chemistry/isolation & purification/pharmacology ; Chymotrypsin/analysis ; Circular Dichroism ; Electrophoresis, Polyacrylamide Gel ; Fabaceae/chemistry ; Molecular Weight ; Seeds/chemistry ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Trypsin/analysis
Keywords	ammonium sulfate ; binding capacity ; cation exchange ; chymotrypsin ; databases ; fenugreek ; gel chromatography ; hydrophobicity ; Kunitz-type proteinase inhibitor ; mass spectrometry ; molecular weight ; pH ; polyacrylamide gel electrophoresis ; polypeptides ; reversed-phase high performance liquid chromatography ; salt concentration ; seeds ; sequence homology ; temperature ; Trigonella foenum-graecum ; trypsin
Language	English
Dates of publication	2013-12
Size	p. 26-36.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	208884-8
ISSN	1873-3700 ; 0031-9422
ISSN (online)	1873-3700
ISSN	0031-9422
DOI	10.1016/j.phytochem.2013.09.010
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The PE16 (Rv1430) of Mycobacterium tuberculosis is an esterase belonging to serine hydrolase superfamily of proteins.

Rafiya Sultana / Mani Harika Vemula / Sharmishta Banerjee / Lalitha Guruprasad

PLoS ONE, Vol 8, Iss 2, p e

2013 Volume 55320

Abstract: The PE and PPE multigene families, first discovered during the sequencing of M. tuberculosis H37Rv genome are responsible for antigenic variation and have been shown to induce increased humoral and cell mediated immune response in the host. Using the ... ...

Abstract	The PE and PPE multigene families, first discovered during the sequencing of M. tuberculosis H37Rv genome are responsible for antigenic variation and have been shown to induce increased humoral and cell mediated immune response in the host. Using the bioinformatics tools, we had earlier reported that the 225 amino acid residue PE-PPE domain (Pfam: PF08237) common to some PE and PPE proteins has a "serine α/β hydrolase" fold and conserved Ser, Asp and His catalytic triad characteristic of lipase, esterase and cutinase activities. In order to prove experimentally that PE-PPE domain is indeed a serine hydrolase, we have cloned the full-length Rv1430 and its PE-PPE domain into pET-28a vector, expressed the proteins in E. coli and purified to homogeneity. The activity assays of both purified proteins were carried out using p-nitrophenyl esters of aliphatic carboxylic acids with varying chain length (C2-C16) to study the substrate specificity. To characterize the active site of the PE-PPE domain, we mutated the Ser199 to Ala. The activity of the protein in the presence of serine protease inhibitor- PMSF and the mutant protein were measured. Our results reveal that Rv1430 and its PE-PPE domain possess esterase activity and hydrolyse short to medium chain fatty acid esters with the highest specific activity for pNPC6 at 37°C, 38°C and pH 7.0, 8.0. The details of this work and the observed results are reported in this manuscript.
Keywords	Medicine ; R ; Science ; Q
Subject code	572
Language	English
Publishing date	2013-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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